What year LS400? If it's an early one from the 90's, you have no worries about immobilisers.
Gloverman is the king of transplants here; he'll probably jump in and let you know what bits you should salvage from the LS400 before you send it to the crusher.
Me, for a motorsport application like yours, I'd probably start from scratch with a new gen MS3, or something similar and not worry about getting the OEM ECU to work. The Toyota/Lexus ECU's are not very tuner friendly and can't be remapped very easily.